Divergent host responses during primary simian immunodeficiency virus SIVsm infection of natural sooty mangabey and nonnatural rhesus macaque hosts

To understand how natural sooty mangabey hosts avoid AIDS despite high levels of simian immunodeficiency virus (SIV) SIVsm replication, we inoculated mangabeys and nonnatural rhesus macaque hosts with an identical inoculum of uncloned SIVsm. The unpassaged virus established infection with high-level viral replication in both macaques and mangabeys. A species-specific, divergent immune response to SIV was evident from the first days of infection and maintained in the chronic phase, with macaques showing immediate and persistent T-cell proliferation, whereas mangabeys displayed little T-cell proliferation, suggesting subdued cellular immune responses to SIV. Importantly, only macaques developed (CD4+)-T-cell depletion and AIDS, thus indicating that in mangabeys limited immune activation is a key mechanism to avoid immunodeficiency despite high levels of SIVsm replication. These studies demonstrate that it is the host response to infection, rather than properties inherent to the virus itself, that causes immunodeficiency in SIV-infected nonhuman primates.     

Impact of host cell line adaptation on quasispecies composition and glycosylation of influenza A virus hemagglutinin

The genome of influenza A viruses is constantly changing (genetic drift) resulting in small, gradual changes in viral proteins. Alterations within antibody recognition sites of the viral membrane glycoproteins hemagglutinin (HA) and neuraminidase (NA) result in an antigenetic drift, which requires the seasonal update of human influenza virus vaccines. Generally, virus adaptation is necessary to obtain sufficiently high virus yields in cell culture-derived vaccine manufacturing. In this study detailed HA N-glycosylation pattern analysis was combined with in-depth pyrosequencing analysis of the virus genomic RNA. Forward and backward adaptation from Madin-Darby Canine Kidney (MDCK) cells to African green monkey kidney (Vero) cells was investigated for two closely related influenza A virus PR/8/34 (H1N1) strains: from the National Institute for Biological Standards and Control (NIBSC) or the Robert Koch Institute (RKI). Furthermore, stability of HA N-glycosylation patterns over ten consecutive passages and different harvest time points is demonstrated. Adaptation to Vero cells finally allowed efficient influenza A virus replication in Vero cells. In contrast, during back-adaptation the virus replicated well from the very beginning. HA N-glycosylation patterns were cell line dependent and stabilized fast within one (NIBSC-derived virus) or two (RKI-derived virus) successive passages during adaptation processes. However, during adaptation new virus variants were detected. These variants carried "rescue" mutations on the genomic level within the HA stem region, which result in amino acid substitutions. These substitutions finally allowed sufficient virus replication in the new host system. According to adaptation pressure the composition of the virus populations varied. In Vero cells a selection for "rescue" variants was characteristic. After back-adaptation to MDCK cells some variants persisted at indifferent frequencies, others slowly diminished and even dropped below the detection limit.     

Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host

The existence of genetic variation for resistance in host populations is assumed to be essential to the spread of an emerging virus. Models predict that the rate of spread slows down with the increasing frequency and higher diversity of resistance alleles in the host population. We have been using the experimental pathosystem Arabidopsis thaliana—tobacco etch potyvirus (TEV) to explore the interplay between genetic variation in host''s susceptibility and virus diversity. We have recently shown that TEV populations evolving in A. thaliana ecotypes that differ in susceptibility to infection gained within-host fitness, virulence and infectivity in a manner compatible with a gene-for-gene model of host–parasite interactions: hard-to-infect ecotypes were infected by generalist viruses, whereas easy-to-infect ecotypes were infected by every virus. We characterized the genomes of the evolved viruses and found cases of host-driven convergent mutations. To gain further insights in the mechanistic basis of this gene-for-gene model, we have generated all viral mutations individually as well as in specific combinations and tested their within-host fitness effects across ecotypes. Most of these mutations were deleterious or neutral in their local ecotype and only a very reduced number had a host-specific beneficial effect. We conclude that most of the mutations fixed during the evolution experiment were so by drift or by selective sweeps along with the selected driver mutation. In addition, we evaluated the ruggedness of the underlying adaptive fitness landscape and found that mutational effects were mostly multiplicative, with few cases of significant epistasis.     

Complex inheritance of larval adaptation in Plutella xylostella to a novel host plant

Studying the genetics of host shifts and range expansions in phytophagous insects contributes to our understanding of the evolution of host plant adaptation. We investigated the recent host range expansion to pea, in the pea-adapted strain (P-strain) of the crucifer-specialist diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae). Larval survivorship on the novel host plant pea and a typical crucifer host (kale) was measured in reciprocal F(1), F(2) and backcrosses between the P-strain and a strain reared only on crucifers (C-strain). Reciprocal F(1) hybrids differed: offspring from P-strain mothers survived better on pea, indicating a maternal effect. However, no evidence for sex-linkage was found. Backcrosses to the P-strain produced higher survivorship on pea than C-strain backcrosses, suggesting recessive inheritance. In a linkage analysis with amplified fragment length polymorphism markers using P-strain backcrosses, two, four and five linkage groups contributing to survival on pea were identified in three different families respectively, indicating oligogenic inheritance. Thus, the newly evolved ability to survive on pea has a complex genetic basis, and the P-strain is still genetically heterogeneous and not yet fixed for all the alleles enabling it to survive on pea. Survivorship on kale was variable, but not related to survivorship on pea. This pattern may characterize the genetic inheritance of early host plant adaptation in oligophagous insect species.     

Mechanisms for adaptation of simian immunodeficiency virus to replication in alveolar macrophages

In contrast to the simian immunodeficiency virus SIVmac239, which replicates poorly in rhesus monkey alveolar macrophages, a variant with nine amino acid changes in envelope (SIVmac239/316E) replicates efficiently and to high titer in these same cells. We examined levels of viral DNA, RNA, antigen, and infectious virus to identify the nature of the block to SIVmac239 replication in these cells. Low levels of viral antigen (0.1 to 1.0 ng of p27 per ml) and infectious virus (100 to 1,000 infectious units per ml) were produced in the supernatant 1 to 4 days after SIVmac239 infection, but these levels did not increase subsequently. SIVmac239 DNA was synthesized in these macrophage cultures during the initial 24 h after infection, but the levels did not increase subsequently. Quantitation of the numbers of infectious cells in cultures over time and the results of experiments in which cells were reexposed to SIVmac239 after the initial exposure indicated that only a small proportion of cells were susceptible to SIVmac239 infection in these alveolar macrophage cultures and that the vast majority (>95%) of cells were refractory to SIVmac239 infection. In contrast to the results with SIVmac239, the levels of viral antigen, infectious virus, and viral DNA increased exponentially 2 to 7 days after infection by SIVmac239/316E, reaching levels greater than 100 ng of p27 per ml and 100,000 infectious units per ml. Since SIVmac239/316E has previously been described as a virus capable of infecting cells in a relatively CD4-independent fashion, we examined the levels of CD4 expression on the surface of fresh and cultured alveolar macrophages from rhesus monkeys. The levels of CD4 expression were extremely low, below the limit of detection by flow cytometry, on greater than 99% of the macrophages. CCR5(+) cells were profoundly depleted only from alveolar macrophage cultures infected with SIVmac239/316E. High concentrations of an antibody to CD4 delayed but did not block replication of SIVmac239/316E. The results suggest that the adaptation of SIVmac316 to efficient replication in alveolar macrophages results from its ability to infect these cells in a CD4-independent fashion or in a CD4-dependent fashion even at extremely low levels of surface CD4 expression. Since resident macrophages in brains and lungs of humans also express little or no CD4, our findings predict the presence of human immunodeficiency virus type 1 that is relatively CD4 independent in the lung and brain compartments of infected people.     

Restrictions to the adaptation of influenza a virus h5 hemagglutinin to the human host

The binding specificities of a panel of avian influenza virus subtype H5 hemagglutinin (HA) proteins bearing mutations at key residues in the receptor binding site were investigated. The results demonstrate that two simultaneous mutations in the receptor binding site resulted in H5 HA binding in a pattern similar to that shown by human viruses. Coexpression of the ion channel protein, M2, from most avian and human strains tested protected H5 HA conformation during trafficking, indicating that no genetic barrier to the reassortment of the H5 surface antigen gene with internal genes of human viruses existed at this level.     

Molecular and biological analyses of quasispecies during evolution of a virulent simian immunodeficiency virus, SIVsmmPBj14.

A prototypic simian immunodeficiency virus (SIVsmm9), isolated from a naturally infected sooty mangabey (Cercocebus atys), was passaged in vivo in a pig-tailed macaque (Macaca nemestrina) having the identifier PBj. When PBj died of a typical AIDS-like syndrome 14 months after infection, the virus isolated from its tissues was subsequently shown to differ from SIVsmm9 genetically and biologically. Most notably, this isolate, SIVsmmPBj14 (SIV-PBj14), is the most virulent primate lentivirus known: it induces acute disease and death within 6 to 10 days after intravenous inoculation into pig-tailed macaques. Between the time of infection with SIVsmm9 and isolation of SIV-PBj14, isolates were obtained periodically from peripheral blood mononuclear cells of PBj. To establish the temporal relationship between evolution of new biologic properties and fixation of specific mutations in the virus population, these sequential SIV-PBj isolates were characterized for unique properties of SIV-PBj14 that appeared to correlate with acute lethal disease. These properties included the ability to replicate in quiescent macaque peripheral blood mononuclear cells, to activate and induce proliferation of CD4+ and CD8+ cells, and to exhibit cytopathicity for mangabey CD4+ lymphocytes. Consistent with earlier studies, a major change in biologic properties occurred between 6 (SIV-PBj6) and 10 (SIV-PBj10) months, with the SIV-PBj8 quasispecies exhibiting properties of both earlier and later isolates. Multiple biologic clones derived from the 6-, 8-, and 10-month isolates also exhibited diverse phenotypes. For example, one SIV-PBj10 biologic clone resembled SIVsmm9 phenotypically, whereas three other biologic clones resembled SIV-PBj14. To evaluate genetic changes, proviral DNA of the biologic clones generated from SIV-PBj6, -PBj8, and -PBj10 was amplified by PCR in the U3 enhancer portion of the long terminal repeats (LTR) and the V1 region of env, where the greatest nucleotide diversity between SIVsmm9 and SIV-PBj14 resided. Nucleotide sequence data indicated that all biologically cloned viruses are distinct and that insertions/duplications of 3 to 27 nucleotides (in multiples of three) had accumulated stepwise in the env V1 region, beginning with SIV-PBj8. In addition, one of four SIV-PBj8 biologic clones had a 22-bp duplication in the LTR which is characteristic of SIV-PBj14. When virus mixtures containing different proportions of two SIV-PBj10 biologic clones with opposite phenotypes were tested, the SIV-PBj14 phenotype was clearly dominant, since mixtures with as few as 10% of the viruses being SIV-PBj14-like exhibited all the properties of the lethal isolate.(ABSTRACT TRUNCATED AT 400 WORDS)     

Zoite migration during infection: parasite adaptation to host defences

The apicomplexan parasite Eimeria tenella has evolved a number of strategies for migration into different compartments of the intestinal tissue during its life cycle. These migration events are associated intricately with pathogenesis and are currently of great interest to coccidiologists. Using evidence from in vivo studies and recent work on the dynamics of gut cell turnover, Peter Daszak suggests that E. tenella zoite migration might be viewed as parasite evolutionary adaptation to evade the host innate immune responses (resistance) and deal with the complex, dynamic nature of gut epithelial tissue.     

Detection and partial characterization of simian immunodeficiency virus SIVsm strains from bush meat samples from rural Sierra Leone

Human immunodeficiency virus type 2 (HIV-2) originated from simian immunodeficiency viruses (SIVs) that naturally infect sooty mangabeys (SMs; Cercocebus atys). In order to further investigate the relationship between HIV-2 and SIVsm, the SIV specific to the SM, we characterized seven new SIVsm strains from SMs sold in Sierra Leone markets as bush meat. The gag, pol, and env sequences showed that, while the viruses of all seven SMs belonged to the SIVsm-HIV-2 lineage, they were highly divergent viruses, in spite of the fact that most of the samples originated from the same geographical region. They clustered in three lineages, two of which have been previously reported. Two of the new SIVsm strains clustered differently in gag and env phylogenetic trees, suggesting SIVsm recombination that had occurred in the past. In spite of the fact that our study doubles the number of known SIVsm strains from wild SMs, none of the simian strains were close to the groups in which HIV-2 was epidemic (groups A and B).     

The threshold bootstrap clustering: a new approach to find families or transmission clusters within molecular quasispecies

Background

Phylogenetic methods produce hierarchies of molecular species, inferring knowledge about taxonomy and evolution. However, there is not yet a consensus methodology that provides a crisp partition of taxa, desirable when considering the problem of intra/inter-patient quasispecies classification or infection transmission event identification. We introduce the threshold bootstrap clustering (TBC), a new methodology for partitioning molecular sequences, that does not require a phylogenetic tree estimation.

Methodology/Principal Findings

The TBC is an incremental partition algorithm, inspired by the stochastic Chinese restaurant process, and takes advantage of resampling techniques and models of sequence evolution. TBC uses as input a multiple alignment of molecular sequences and its output is a crisp partition of the taxa into an automatically determined number of clusters. By varying initial conditions, the algorithm can produce different partitions. We describe a procedure that selects a prime partition among a set of candidate ones and calculates a measure of cluster reliability. TBC was successfully tested for the identification of type-1 human immunodeficiency and hepatitis C virus subtypes, and compared with previously established methodologies. It was also evaluated in the problem of HIV-1 intra-patient quasispecies clustering, and for transmission cluster identification, using a set of sequences from patients with known transmission event histories.

Conclusion

TBC has been shown to be effective for the subtyping of HIV and HCV, and for identifying intra-patient quasispecies. To some extent, the algorithm was able also to infer clusters corresponding to events of infection transmission. The computational complexity of TBC is quadratic in the number of taxa, lower than other established methods; in addition, TBC has been enhanced with a measure of cluster reliability. The TBC can be useful to characterise molecular quasipecies in a broad context.     

Sympatric host races of the European corn borer: adaptation to host plants and hybrid performance

The European corn borer (ECB), Ostrinia nubilalis, is a major pest of maize crops. In Europe, two sympatric host races are found: one feeds on maize (Zea mays) and the other mainly on mugwort (Artemisia vulgaris). The two host races are genetically differentiated, seldom crossing in the laboratory or in the field, and females preferentially lay eggs on their native host species. We conducted two independent experiments, in field and greenhouse conditions, to determine whether the two host races are locally adapted to their host species. The effect of larval density and the performance of hybrids were also investigated. Despite some differences in overall larval feeding performance, both experiments revealed consistent patterns of local adaptation for survival and for larval weight in males. In females the same trend was observed but with weaker statistical support. F1 hybrids did not seem to be disadvantaged compared with the two parental races. Overall, our results showed that both host races are physiologically adapted to their native host. The fitness trade-off between the two host plants provides a potential driving force for ecological speciation in this species.     

Evolution of black yeasts: possible adaptation to the human host

Ascomycetous black yeasts show adaptations to a wide array of environmental conditions. Dothideaceous black yeasts are mostly found on plant leaves, while among herpotrichiellaceous species there are numerous opportunists on humans.Factors which are of ecological significance include the presence of melanin and carotene, formation of thick cell walls and meristematic growth, presence of yeast-like phases, presence of additional forms of conidiogenesis, thermo- and osmotolerance, adhesion, hydrophobicity, production of extracellular polysaccharides, siderophores and acidic or alkaline secondary metabolites.The potential pathogenicity of a species is partly determined by its natural ecological niche. Dothideaceous black yeasts are osmotolerant rather than pathogenic. Herpotrichiellaceous black yeasts probably have low competitive ability and are found in rather special niches as secondary saprophytes, e.g., on bacterial mats, on other fungi or in poor environments. Some species possibly utilize animal vectors for dispersal.     

Frequent conjugative transfer accelerates adaptation of a broad-host-range plasmid to an unfavorable Pseudomonas putida host

IncP-1 plasmids are known to be promiscuous, but it is not understood if they are equally well adapted to various species within their host range. Moreover, little is known about their fate in bacterial communities. We determined if the IncP-1beta plasmid pB10 was unstable in some Proteobacteria, and whether plasmid stability was enhanced after long-term carriage in a single host and when regularly switched between isogenic hosts. Plasmid pB10 was found to be very unstable in Pseudomonas putida H2, and conferred a high cost (c. 20% decrease in fitness relative to the plasmid-free host). H2(pB10) was then evolved under conditions that selected for plasmid maintenance, with or without regular plasmid transfer (host-switching). When tested in the ancestral host, the evolved plasmids were more stable and their cost was significantly reduced (9% and 16% for plasmids from host-switched and nonswitched lineages, respectively). Our findings suggest that IncP-1 plasmids can rapidly adapt to an unfavorable host by improving their overall stability, and that regular conjugative transfer accelerates this process.     

Escherichia coli physiology and metabolism dictates adaptation to diverse host microenvironments

Bacterial growth in the host is required for pathogenesis. To successfully grow in vivo, pathogens have adapted their metabolism to replicate in specific host microenvironments. These adaptations reflect the nutritional composition of their host niches, inter-bacterial competition for carbon and energy sources, and survival in the face of bactericidal defense mechanisms. A subgroup of Escherichia coli, which cause urinary tract infection, bacteremia, sepsis, and meningitis, have adapted to grow as a harmless commensal in the nutrient-replete, carbon-rich human intestine but rapidly transition to pathogenic lifestyle in the nutritionally poorer, nitrogen-rich urinary tract. We discuss bacterial adaptations that allow extraintestinal pathogenic E. coli to establish both commensal associations and virulence as the bacterium transits between disparate microenvironments within the same individual.     

Local adaptation and host race formation of a gall-forming aphid in relation to environmental heterogeneity

Summary The process of host race formation in the aphid Tetraneura yezoensis is examined in relation to its population structure. T. yezoensis induces pouch galls on new leaves of Ulmus davidiana and U. laciniata. Its populations on the two host species are often sympatric. Fundatrices found on one elm species, when reciprocally transplanted to the other, suffered greatly reduced average fitness. This shows that aphid populations associated with the two elm species are genetically differentiated in physiological traits. Individual trees of each elm species showed large differences in susceptibility to gall formation and in bud burst time, and such between-tree variations were consistent over years. Overwintered eggs taken in early spring from four trees (two from each species) were incubated under the same temperature conditions. The average hatching time differed significantly even between populations from conspecific trees, and the sequence of egg hatching paralleled that of the leafing of those four trees. This between-tree difference in hatching time was consistent over years and was found to be genetic, showing that gene flow between aphid populations on separate trees is often restricted. The heterogeneity in host traits may have promoted the evolution of philopatry in this aphid. Of the fundatrices that hatched on a tree of one elm species, a few precent were preadapted to gall formation on the other elm species. This suggests that the formation of a new host race proceeds parapatrically under disruptive selection and at a low level of gene flow. Evidence was actually obtained that a small fraction of Tetraneura alates are passively transported and land on non-host plants.     

A history of phenotypic plasticity accelerates adaptation to a new environment

Can a history of phenotypic plasticity increase the rate of adaptation to a new environment? Theory suggests it can be through two different mechanisms. Phenotypically plastic organisms can adapt rapidly to new environments through genetic assimilation, or the fluctuating environments that result in phenotypic plasticity can produce evolvable genetic architectures. In this article, I studied a model of a gene regulatory network that determined a phenotypic character in one population selected for phenotypic plasticity and a second population in a constant environment. A history of phenotypic plasticity increased the rate of adaptation in a new environment, but the amount of this increase was dependent on the strength of selection in the original environment. Phenotypic variance in the original environment predicted the adaptive capacity of the trait within, but not between, plastic and nonplastic populations. These results have implications for invasive species and ecological studies of rapid adaptation.     

Charting the host adaptation of influenza viruses

Four influenza pandemics have struck the human population during the last 100 years causing substantial morbidity and mortality. The pandemics were caused by the introduction of a new virus into the human population from an avian or swine host or through the mixing of virus segments from an animal host with a human virus to create a new reassortant subtype virus. Understanding which changes have contributed to the adaptation of the virus to the human host is essential in assessing the pandemic potential of current and future animal viruses. Here, we develop a measure of the level of adaptation of a given virus strain to a particular host. We show that adaptation to the human host has been gradual with a timescale of decades and that none of the virus proteins have yet achieved full adaptation to the selective constraints. When the measure is applied to historical data, our results indicate that the 1918 influenza virus had undergone a period of preadaptation prior to the 1918 pandemic. Yet, ancestral reconstruction of the avian virus that founded the classical swine and 1918 human influenza lineages shows no evidence that this virus was exceptionally preadapted to humans. These results indicate that adaptation to humans occurred following the initial host shift from birds to mammals, including a significant amount prior to 1918. The 2009 pandemic virus seems to have undergone preadaptation to human-like selective constraints during its period of circulation in swine. Ancestral reconstruction along the human virus tree indicates that mutations that have increased the adaptation of the virus have occurred preferentially along the trunk of the tree. The method should be helpful in assessing the potential of current viruses to found future epidemics or pandemics.     

Transposable elements and adaptation of host bacteria

A transposable element (TE) is a mobile sequence present in the genome of an organism. TEs can cause lethal mutations by inserting into essential, genes, promoting deletions or leaving short sequences upon excision. They therefore may be gradually eliminated from mixed populations of haploid micro-organisms such asEscherichia coli if they cannot balance this mutation load. Horizontal transmission between cells is known to occur and promote the transfer of TEs, but at rates often too low to compensate for the burden to their hosts. Therefore, alternative mechanisms should be found by these elements to earn their keep in the cells. Several theories have been suggested to explain their long-term maintenance in prokaryotic genomes, but little molecular evidence has been experimentally obtained. In this paper, the permanence of transposable elements in bacterial populations is discussed in terms of costs or benefits for the element and for the host. It is observed that, in all studies yet reported, the elements do not behave in their host as selfish DNA but as a co-operative component for the evolution of the couple.